Staphylococcus aureus infections are often associated with high rates of morbidity and mortality (see Shorr et al., Crit Care Med, 34: 2588-2595 (2006)). Indeed, reports estimate that in 2005 the organism caused more U.S. deaths than HIV/AIDS (see Bancroft, E. A., Jama, 298: 1803-1804 (2007); Klevens et al., Jama, 298: 1763-1771 (2007)). The emergence of vancomycin-resistant, methicillin-resistant, multidrug-resistant, and hypervirulent strains has further accentuated the need for novel antibiotics (see Appelbaum, P. C., Int J Antimicrob Agents, 30: 398-408 (2007); Zetola et al., Lancet Infect Dis, 5: 275-286 (2005)). Bacterial RNA processing and degradation are required cellular processes that can be exploited for antimicrobial drug discovery.
Much of the understanding of bacterial RNA degradation comes from studies of Escherichia coli where bulk mRNA decay is thought to be catalyzed by a holoenzyme complex (RNA degradosome), which consists of at least four subunits: RNase E (rne), RNA helicase (rhlB), enolase (eno), and PNPase (pnpA) (see Carpousis, A. J., Annu Rev Microbiol, 61: 71-87 (2007)). RNase E is an essential ribonuclease and a key component of the degradosome complex. It serves as a scaffold for the assembly of other members of the RNA degradosome and catalyzes the initial endoribonucleolytic event during substrate degradation (see Mackie, G. A., Nature, 395: 720-723 (1998); Vanzo et al., Genes Dev, 12: 2770-2781 (1998)). Based on its essentiality, RNase E could be considered an appropriate target for antibiotic drug discovery. However, many Gram-positive bacteria, including S. aureus, lack an RNase E amino acid ortholog (see Condon, C., Microbiol Mol Biol Rev, 67: 157-174 (2003)). As a consequence, their degradation components and mechanism(s) of mRNA decay are less understood.
Recent studies suggest that at least two ribonucleases, RNase J1 and RNase Y, contribute to bulk mRNA degradation within Bacillus subtilis, and presumably other Gram-positive bacteria. B. subtilis ribonuclease J1 is a bifunctional ribonuclease, with 5′ exonuclease and endonuclease activities, that mediates mRNA degradation in vitro (see Even et al., Nucleic Acids Res, 33: 2141-2152 (2005); Mathy et al., Cell, 129: 681-692 (2007)). The enzyme has also been found to interact with enolase (a component of the E. coli RNA degradosome) and RNase J1 depleted B. subtilis strains demonstrate a moderate decrease in mRNA decay, suggesting that it may be the functional equivalent to E. coli RNase E (see Even et al., Nucleic Acids Res, 33: 2141-2152 (2005); Commichau et al., Mol Cell Proteomics, 8: 1350-1360 (2009); Mader et al., Mol Microbiol, 70: 183-196 (2008)). However, mRNA turnover still occurs in RNase J1 diminished cells and RNA species containing 5′ strong-hairpin structures are not effectively degraded by the enzyme, indicating that additional factors are likely to contribute to B. subtilis cellular RNA degradation (see Yao et al., Rna, 15: 2331-2339 (2009)). Ribonuclease Y is a recently identified endonuclease that may ostensibly work in concert with RNase J1 to mediate bulk RNA decay. RNase Y can cleave mRNA molecules containing high-order secondary structures and globally affects cellular messenger RNA turnover (see Shahbabian et al., Embo J, 28: 3523-3533 (2009)). Both RNase J1 and RNase Y are essential enzymes and, in that regard, could be considered targets for antimicrobial drug discovery (see Kobayashi et al., Proc Natl Acad Sci USA, 100: 4678-4683 (2003)). However, it remains to be seen whether RNase J1, RNase Y, and/or previously uncharacterized ribonucleases modulate mRNA decay within S. aureus. 